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I have a 2007 Unlimited and has the same problem. My Jeep is a soft top and the water came from the rain and a poor seal of the back window. Part of the problem came from the displacement of the plastic "c" shaped "rear window bar holder" that clips on to the rear on either side of rear window. Ocasionally the clip pops out of place and breaks the seal between the rubber on the window and the rear sides of the Jeep.

Sealant alone will not stop a leak where the luggage rack is leaking, if it is the L/R. I am a Pilot and you just cant imagine how water can be driven in past sealant at speed. If you are leaving it to the dealer to correct this leak, good luck. I really believe it is the rack. A window leak is to easy to correct.

where inside the jeep is it wet? I believe the unlimited model was all removable hard top. any way check the seals around the removable top and at the windows. but that is the best i can do w/out knowing where inside your jeep it's wet.

Maybe. If you have a fixed antenna on that side of the vehicle, the large rubber gromet on the wire leading into the passenger compartment may have come out, allowing lots of rain water to enter the vehicle. Happened on my 94 and flooded the passenger side.